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Protein Crystallography Newsletter
Volume 5, No. 5, May 2013
In this issue:
Crystallography in the news
Science video of the month
Product video of the month
Product spotlight: PlateMate
Lab spotlight: Guarné and Junop labs
Useful links for crystallography
Upcoming event of note
Survey of the month
Monthly crystallographic papers
Book review
Science Video of the Month Structural biology at McGill - where biology and
medicine intersect
https://www.youtube.com/watch?v=xvNfrYb81Vs
McGill Biochemistry Prof. Kalle Gehring and colleaguesat McGill, in partnership with the University ofMontreal, have been awarded a combined $11 millionfrom CFI, the Quebec Government and partners topurchase equipment enabling them to visualize thethree-dimensional shapes of biological molecules, likeproteins and nucleic acids. This should lead to a betterunderstanding of the origins of diseases such ascancer and to the design of novel molecules for use instructure-based drug design and green chemistry.
Product Video of the Month
Crystallography in the news
May 1, 2013. Greg Hura, Helen Budworth and Cynthia McMurray, all researchers withthe U.S. Department of Energy's Lawrence Berkeley National Laboratory, developed astructural comparison map for SAXS imaging and tested it on a chemotherapeutictarget protein. This technique enables researchers at a glance to identify structuralsimilarities and differences between multiple proteins under a variety of conditions.
May 6, 2013. Proteros Biostructures GmbH announced the successful completion of anintegrated lead discovery collaboration with Eisai Co., Ltd. Based on Proteros' structureguided discovery platform, various series of Lead Compounds were developed within aperiod of 10 months.
May 9, 2013. McGill University researchers have unlocked a new door to developingdrugs to slow the progression of Parkinson's disease. Collaborating teams led by Dr.Edward A. Fon at the Montreal Neurological Institute and Hospital -The Neuro, and Dr.Kalle Gehring in the Department of Biochemistry at the Faculty of Medicine, havediscovered the three-dimensional structure of the protein Parkin. Mutations in Parkincause a rare hereditary form of Parkinson's disease and are likely to also be involved inmore commonly occurring forms of Parkinson's disease.
May 17, 2013. Bryan Roth's laboratory at the University of North Carolina has teamedup with Ray Stevens' group at Scripps as part of the NIGMS Protein StructureInitiative. For this new project involving serotonin receptors, the two labs also workedwith the laboratories of Professors Eric Xu and Hualiang Jiang at the Shanghai Instituteof Materia Medica, part of the Chinese Academy of Sciences.
May 17, 2013. Protein conformation studies by a collaboration of researchers in Japanidentify changes in protein shape that contribute to autophagy, a major system fordegrading cellular material and maintaining cells. The results clarify stages in autophagythat were previously a mystery. Ohsumi, Sakoh-Nakatogawa and colleagues at TokyoInstitute of Technology, Institute of Microbial Chemistry and Hokkaido University usedbiochemical assays, X-ray crystallography and mutational analyses to study theconformation of the proteins and how their activities changed for different mutantvariants of the proteins.
May 22, 2013. Mig AG and BioMed Partners have injected an additional €9.5m intoGermany-based SuppreMol, alongside a number of other backers in an extension of thecompany's series-D funding round. SuppreMol was founded in Martinsried in 2002 by ateam of protein crystallography experts from the Max Planck Institute of Biochemistry.The company currently employs 18 staff.
May 27, 2013. Research workers at the Max Planck Institute for Biophysical Chemistryin Göttingen and Freie Universität Berlin have elucidated a previously unknownmechanism that regulates one of the essential processes accompanying geneexpression in higher organisms. In humans, errors in this control mechanism can lead toblindness. Sina Mozaffari-Jovin and Cindy Will from the research group of ReinhardLührmann in Göttingen discovered that the helicase activity of Brr2 is inhibited by aparticular part of another protein of the spliceosome, Prp8. Traudy Wandersleben andKarine Santos from the research group of Markus Wahl in Berlin determined the atomicstructure of the Brr2 protein in contact with the relevant regulatory portion of Prp8.
May 28, 2013. Using a technique called fluctuation X-ray scattering (fXS), Peter Zwartand his colleagues at the U.S. Department of Energy's Lawrence Berkeley NationalLaboratory, working with collaborators from Arizona State University, the University ofWisconsin-Milwaukee, and DOE's Pacific Northwest National Laboratory, have shownthat data obtained employing free-electron lasers can yield low-resolution shapes of
biomolecules in close to their natural state with much greater confidence than iscurrently possible with less powerful synchrotron light sources.
Rigaku PlateMate demonstration video.
Lab in the Spotlight
Guarné & Junop labs @ McMaster University
Survey of the Month
Product spotlight: Rigaku PlateMate
You can easily screen your crystals directly in crystallizationplates with the Rigaku PlateMate. The Rigaku PlateMate is anadapter that holds MRC two-well and Greiner low-profilecrystallization plate types and that can be set up on anumber of Rigaku HomeLab systems. The plate slides onlinear rails and fine adjustment knobs control the positionboth horizontally and vertically. Crystals in any of the 96 wellsin the plate can be precisely centered in the X-ray beam.
The PlateMate is an essential tool for easily and rapidly identifying protein crystals versussalt and detergent crystals directly in the plate, and for screening crystals whichdeteriorate as soon as they are taken out of their crystallization environment.
Ask for more information.
Lab in the spotlight: Guarné & Junop labs @ McMaster
Through the Leaders Opportunity Fund from the Canadian Foundation for Innovation,McMaster biochemists Alba Guarné and Murray Junop, a member of the Michael G.DeGroote Institute for Infectious Disease Research, have created a state-of-the-artcrystallization and diffraction facility. The new facility, recently inaugurated, is designedto streamline two bottleneck steps in protein crystallography: protein crystallization andcrystal optimization. It is also equipped to analyze protein crystals by X-ray diffractionand macromolecules in solution using small angle X-ray scattering.
Dr. Guarné is an Associate Professor in Biochemistry and Biomedical Sciences atMcMaster University. Her research interests are focused on understanding howarchitectural proteins determine the fate of DNA in chromosome replication and repair.
Dr. Junop is an Associate Professor in the Department of Biochemistry and BiomedicalSciences. His group is highly active in protein structure determination as a means tofurther our understanding in a variety of biologically and biomedically important areas, inparticular DNA double strand break/repair and the development of new antibiotics.
Useful link: DistilBio
Distilbio: Web-based semantic search and data integration platform. With a focus onsimplicity, DistilBio enables a paradigm shift in the way scientists and decision makerssearch and retrieve data in the life sciences. You can ask questions simply. Forexample, frame your question using the simple interface: e.g. Find Proteins associatedwith Cancer and their Function. A dynamic interface allows you to explore the resultsretrieved for your questions within seconds. You can leverage connections to discovernovel patterns and relationships hidden in the silos of the deep web.
Selected recent crystallographic papers
Structural Basis for Molecular Recognition at Serotonin Receptors. Chong Wang; YiJiang; Jinming Ma; Huixian Wu; Wacker, Daniel; Katritch, Vsevolod; Gye Won Han; WeiLiu; Xi-Ping Huang; Vardy, Eyal; McCorvy, John D.; Xiang Gao; Zhou, X. Edward;Melcher, Karsten; Chenghai Zhang; Fang Bai; Huaiyu Yang; Linlin Yang; Hualiang Jiang;Roth, Bryan L. Science. 5/3/2013, Vol. 340 Issue 6132, p610-614. 5p.http://dx.doi.org/10.1126/science.1232807.
Structural Features for Functional Selectivity at Serotonin Receptors. Wacker, Daniel;Chong Wang; Katritch, Vsevolod; Gye Won Han; Xi-Ping Huang; Vardy, Eyal; McCorvy,
John D.; Yi Jiang; Meihua Chu; Fai Yiu Siu; Wei Liu; Xu, H. Eric; Cherezov, Vadim; Roth,Bryan L.; Stevens, Raymond C. Science. 5/3/2013, Vol. 340 Issue 6132, p615-619. 5p.http://dx.doi.org/10.1126/science.1232808.
Using high-throughput in situ plate screening to evaluate the effect of dehydration onprotein crystals. Douangamath, Alice; Aller, Pierre; Lukacik, Petra; Sanchez-Weatherby,
http://www.surveymonkey.com/s/rigaku
Last Month's Survey Results
In 2011, 1.4 million people died because of TB,with the highest death rate being in Africa.There are estimated to be 630,000 peopleinfected with multidrug-resistant TBworldwide. If new medications are not foundsoon, TB could become an extremely seriouspublic health problem. Many structuralbiologists are involved in TB research. Fromwhat you know or have learned from yourcolleagues, what do think the chances are forfinding a cure for TB is before multidrug-resistant TB becomes a global issue?
Upcoming Event of Note
2013 St Andrews CCP4 ProteinCrystallography Summer School
Closing date is 31st May 2013
protein crystals. Douangamath, Alice; Aller, Pierre; Lukacik, Petra; Sanchez-Weatherby,Juan; Moraes, Isabel; Brandao-Neto, Jose. Acta Crystallographica: Section D. May2013,Vol. 69 Issue 5, p920-923. 4p. http://dx.doi.org/10.1107/S0907444913002412.
Structural biology: Active arrestin proteins crystallized. Borshchevskiy, Valentin; Büldt,Georg. Nature. 5/2/2013, Vol. 497 Issue 7447, p45-46. 2p. 1 Diagram.http://dx.doi.org/10.1038/nature12096.
Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. Barends, Thomas R. M.; Foucar, Lutz; Shoeman, Robert L.; Bari, Sadia;Epp, Sascha W.; Hartmann, Robert; Hauser, Gunter; Huth, Martin; Kieser, Christian;Lomb, Lukas; Motomura, Koji; Nagaya, Kiyonobu; Schmidt, Carlo; Strecker, Rafael;Anielski, Denis; Boll, Rebecca; Erk, Benjamin; Fukuzawa, Hironobu; Hartmann, Elisabeth;Hatsui, Takaki. Acta Crystallographica: Section D. May2013, Vol. 69 Issue 5, p838-842.5p. http://dx.doi.org/10.1107/S0907444913002448.
Crystallographic studies on B12 binding proteins in eukaryotes and prokaryotes.Sukumar, Narayanasami. Biochimie. May2013, Vol. 95 Issue 5, p976-988. 13p.http://dx.doi.org/10.1016/j.biochi.2013.01.014.
Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trappedfolding intermediates. Koharudin, Leonardus M. I.; Lin Liu; Gronenborn, Angela M.Proceedings of the National Academy of Sciences of the United States of America.5/7/2013, Vol. 110 Issue 19, p7702-7707. 6p.http://dx.doi.org/10.1073/pnas.1300327110.
Probing hemoglobin confinement inside submicron silica tubes using synchrotron SAXSand electrochemical response. Mandal, Soumit; Nagarajan, Brindha; Amenitsch, H.;Bhattacharyya, Aninda. European Biophysics Journal. May2013, Vol. 42 Issue 5, p371-382. 12p. http://dx.doi.org/10.1007/s00249-013-0886-0.
Structural Characterization of H-l Parvovirus: Comparison of Infectious Virions to EmptyCapsids. Haider, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle;Dlnsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis.Journal of Virology. May2013, Vol. 87 Issue 9, p5128-5140. 13p.http://dx.doi.org/10.1128/JVI.03416-12.
Structural investigations of recombinant urokinase growth factor-like domain.Beloglazova, I.; Beabealashvilli, R.; Gursky, Ya.; Bocharov, E.; Mineev, K.; Parfenova, E.;Tkachuk, V. Biochemistry. May2013, Vol. 78 Issue 5, p517-530. 14p.http://dx.doi.org/10.1134/S0006297913050106.
Structural and stability studies of the human mtHsp70-escort protein 1: An essentialmortalin co-chaperone. Dores-Silva, P.R.; Minari, K.; Ramos, C.H.I.; Barbosa, L.R.S.;Borges, J.C. International Journal of Biological Macromolecules. May2013, Vol. 56, p140-148. 9p. http://dx.doi.org/10.1016/j.ijbiomac.2013.02.009.
Three Sites and You Are Out: Ternary Synergistic Allostery Controls Aromatic AminoAcid Biosynthesis in Mycobacterium tuberculosis. Blackmore, Nicola J.; Reichau,Sebastian; Jiao, Wanting; Hutton, Richard D.; Baker, Edward N.; Jameson, Geoffrey B.;Parker, Emily J. Journal of Molecular Biology. May2013, Vol. 425 Issue 9, p1582-1592.11p. http://dx.doi.org/10.1016/j.jmb.2012.12.019.
AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips,Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David;Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson,Keith O.; Soltis, S. Michael. Acta Crystallographica: Section D. May2013, Vol. 69 Issue5, p796-803. 8p. http://dx.doi.org/10.1107/S0907444913001984.
Integrated database of information from structural genomics experiments. Asada,Yukuhiko; Sugahara, Michihiro; Mizutani, Hisashi; Naitow, Hisashi; Tanaka, Tomoyuki;Matsuura, Yoshinori; Agari, Yoshihiro; Ebihara, Akio; Shinkai, Akeo; Kuramitsu, Seiki;Yokoyama, Shigeyuki; Kaminuma, Eri; Kobayashi, Norio; Nishikata, Koro; Shimoyama,Sayoko; Toyoda, Tetsuro; Ishikawa, Tetsuya; Kunishima, Naoki. Acta Crystallographica:
Section D. May2013, Vol. 69 Issue 5, p914-919. 6p.http://dx.doi.org/10.1107/S0907444913001728.
Structural biology and cancer. Garratt, Richard. BMC Proceedings. 2013, Vol. 7 IssueSuppl 2, p1-1. 1p. http://www.biomedcentral.com/content/pdf/1753-6561-7-S2-K15.pdf.
On optimal placement of molecules in the unit cell. Dauter, Zbigniew. Acta
The 19th Summer School in ProteinCrystallography will be held at The University of StAndrews. The course aims to cover the theoreticaland practical aspects of protein crystallography fromexpression and purification, through crystal growth todata collection on in-house and synchrotron sources,phasing methods (MAD, SAD, IR, MR using SHELX,PHASER, SOLVE etc.), automated model building andphase extension (e.g. ARP/wARP, BUCCANEER,SHELXE, RESOLVE), refinement (REFMAC, SHELX) andvalidation. Hands-on sessions on data integration(MOSFLM), molecular replacement (CCP4i), MAD/SADphasing (SHELX) and electron density mapinterpretation (COOT) will be included, as well asremote data collection at ESRF.
The course will be taught by a number of tutors withexpertise covering all aspects of the field, includingPete Artymiuk (Sheffield), Wulf Blankenfeldt(Bayreuth), Liz Duke (Diamond), Tracey Gloster (StAndrews), Gordon Leonard (ESRF), Jim Naismith (StAndrews), Garry Taylor (St Andrews) and SteveWood (St George's/UCL).
On optimal placement of molecules in the unit cell. Dauter, Zbigniew. ActaCrystallographica: Section D. May2013, Vol. 69 Issue 5, p872-878. 7p.http://dx.doi.org/10.1107/S0907444913002722.
Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites inSolution. Blanchet, Clement E.; Svergun, Dmitri I. Annual Review of Physical Chemistry.2013, Vol. 64, p37-54. 18p. http://dx.doi.org/10.1146/annurev-physchem-040412-110132.
Small-Angle X-Ray Scattering for Imaging of Surface Layers on Intact Bacteria in theNative Environment. Sekot, Gerhard; Schuster, David; Messner, Paul; Pum, Dietmar;Peterlik, Herwig; Schaffer, Christina. Journal of Bacteriology. May2013, Vol. 195 Issue10, p2408-2414. 7p. http://dx.doi.org/10.1128/JB.02164-12.
The role of structural bioinformatics resources in the era of integrative structuralbiology. Gutmanas, Aleksandras; Oldfield, Thomas J.; Patwardhan, Ardan; Sen,Sanchayita; Velankar, Sameer; Kleywegt, Gerard J. Acta Crystallographica: Section D.May2013, Vol. 69 Issue 5, p710-721. 12p.http://dx.doi.org/10.1107/S0907444913001157.
From gene to structure: The protein factory of the NBICS Centre of KurchatovInstitute. Boyko, K.; Lipkin, A.; Popov, V.; Kovalchuk, M. Crystallography Reports.May2013, Vol. 58 Issue 3, p442-449. 8p.http://dx.doi.org/10.1134/S106377451105004X.
Structural analysis of malaria-parasite lysyl-tRNA synthetase provides a platform for drugdevelopment. Khan, Sameena; Garg, Ankur; Camacho, Noelia; Van Rooyen, Jason;Kumar Pole, Anil; Belrhali, Hassan; Ribas de Pouplana, Lluis; Sharma, Vinay; Sharma,Amit. Acta Crystallographica: Section D. May2013, Vol. 69 Issue 5, p785-795. 11p.http://dx.doi.org/10.1107/S0907444913001923.
Book review:
The Particle at the End of the Universe By Sean Carroll Penguin, 2012. ISBN: 1101609702, 9781101609705
Sean Carroll, in his book The Particle at the End of the Universe: How the Hunt for theHiggs Boson Leads Us to the Edge of a New World, examines the recent "discovery" ofthe Higgs boson and the decades of research and effort that have gone into such arevolutionary moment in science. He offers an inclusive and extensive look into thehistory of the Higgs boson and the particle physics that supported its discovery.
Carroll begins with a rundown of particle physics, particularly an explanation of theStandard Model. The Standard Model involves looking at the breakdown of matter intoits ultimate constituents, quarks and leptons. He details the attempts throughouthistory to smash elementary particles together at increasing energies in order to provethe existence of subatomic particles and study their behaviors. The Standard Modelsuggests that everything in the universe consists of fields: both force fields that pushand pull as well as matter fields whose vibrations are made of particles. The Higgsboson, as proposed by the Standard Model, serves to break symmetries and explainthe behavior of other Standard Model particles in the macrocosm that is the entireuniverse. Because the Higgs boson is such an integral facet in supporting thehypotheses of the Standard Model, its discovery has been taken very seriously andrather slowly. Scientists have spent years hypothesizing how to construct experimentsto find the Higgs boson and once some of those experiments began showing promisingresults, scientists have waited for the data to indicate a high enough statisticalsignificance to warrant the jubilation associated with such a discovery.
He also delves into a discussion of the Large Hardon Collider (LHC), and the years of
effort and policymaking that went into bringing it to life. A number of supercollidershave been built over the years, but none that came to fruition have rivaled the LHC insize and energy capacity in collisions. Interestingly enough, there were plans for aSuperconducting Supercollider (SSC) to be built in Waxahachie, Texas that would haverivaled the LHC in size and energy capacity; however, these plans were never realized.
Carroll addresses the controversial conception that the Higgs boson is the "Godparticle" and argues that this name is largely an attention-seeking misnomer largelyemployed by the press to sell papers, and draws attention to the fact that hedeliberately chose not to use the phrase "God particle" in his tit le. He explains how theHiggs boson has nothing to do with God or religion, and should not play an essential
Higgs boson has nothing to do with God or religion, and should not play an essentialrole in either proving or disproving theological tenets.
The announcement of the discovery of the Higgs boson has been a triumphantmoment in the history of science, but it was the result of a culmination of decades ofeffort and experimentation by dozens of scientists and engineers. This discovery willundoubtedly lead to countless others through the exploration of new symmetries,forces, and dimensions in the universe.
Jeanette S. Ferrara Princeton, Class of 2015
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